rs1368402

Positions:

• chr5-146337722-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001414499.1(LOC127814297):​c.2824-1381A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,020 control chromosomes in the GnomAD database, including 8,370 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (8370 hom., cov: 32)
• Consequence: LOC127814297 NM_001414499.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

Genes affected

ENSG00000275740 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC127814297	NM_001414499.1	c.2824-1381A>C		intron_variant			NP_001401428.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000275740	ENST00000506502.2	c.2947-1381A>C		intron_variant		5		ENSP00000475384.1
ENSG00000250025	ENST00000515598.1	n.404-30446T>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45612 AN: 151902 Hom.: 8341 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.274

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.301 AC: 45686 AN: 152020 Hom.: 8370 Cov.: 32 AF XY: 0.296 AC XY: 21969 AN XY: 74288

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.271

Alfa AF: 0.234 Hom.: 5262

Bravo AF: 0.314

Asia WGS AF: 0.197 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.5
DANN	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1368402; hg19: chr5-145717285;